While CellML versions are not substantially different from each other in terms of the XML element localNames, the changes between 1.0 and 1.1(and likely any future versions) will make backwards compatibility for impossible for most, if not all, CellML processing tools. As such, a new media type for each version is justified. Similarly, the version parameter and the section on determining the version from the XML has been dropped. Both versions of the CellML specification are now referenced as normative references.
I went back and re-read the comments you got, and I think you may have interpreted them incorrectly. I think you were being advised to drop the version parameter, not to register two different media types. The way that you tell the versions apart is to look inside the documents themselves. The approach of registering a new media type every time there's an incompatible change isn't consistent with current practice, and isn't particularly scalable, so I'm uncomfortable setting a precedent that every version of a format should get a different type. Are you saying CellML 1.1 readers can't also read 1.0? Or that future CellML versions will also be incompatible? Is 1.0 deprecated in favor of 1.1, or do you intend to use both forever? Why not just register CellML 1.1 and recommend that people not use CellML 1.0, if 1.1 replaces 1.0? Larry